The two assembly officers are locked in a row over the departure

Dr John Marek, his deputy, wrote to Lord Elis-Thomas, accusing him of plotting the assembly clerk's departure without consulting assembly members.

Paul Silk, 54, is to leave in January after nearly five years in the job.

Lord Elis-Thomas has not yet responded to Dr Marek's letter but paid tribute to Mr Silk's "unique contribution".

Meanwhile, Mr Silk said it was "clear" that someone with a different skill set was wanted for the new chief executive role and decided not to apply.

Dr Marek made public his letter to Lord Elis-Thomas, condemning his handling of the departure of Mr Silk, who acts as principal adviser to the presiding officer.

The AM writes that he is "appalled" at the way Paul has been forced out by Lord Elis Thomas.

In many ways, I am very sorry that I will not be part of the very exciting future of the assembly Paul Silk

It had been expected Mr Silk would continue to manage the 280 staff transferring over to the new assembly commission from next May.

Staff working for the assembly itself - as distinct from the assembly government - will cease to be members of the Welsh government's civil service.

Dr Marek writes: "The assembly will need his (Mr Silk's) services when primary legislation passes through the various procedures in the assembly. Those are the extra duties we will have as an assembly, there will be no other significant new responsibilities.

He adds that "a chief executive appointment, probably from local government, will put us on a level with other county councils".

He also accuses the presiding officer of "plotting" to make the decision during August, when assembly members are not sitting.

Lord Elis-Thomas earlier issued a statement recording his "warmest thanks to Paul for his unique contribution in developing the assembly parliamentary service, which has prepared us so well for implementing the Government of Wales Act 2006".

Crickhowell-born Mr Silk will be returning to the Commons where he previously worked between 1975 and 1977 and 1979 and 2001, when he moved to the assembly role.

He explained his decision to go saying that it was clear to him that "someone with a different skill set from mine" was being sought to take on the new post of chief executive and assembly clerk of which is to be advertised shortly.

Mr Silk added: "I can understand this. I have therefore decided that I shall not apply for the post.

He said: "In many ways, I am very sorry that I will not be part of the very exciting future of the assembly.

"But I believe that I have done something since I arrived in March 2001 to build up a parliamentary organisation which can take its proper place among the legislatures of the United Kingdom, " Mr Silk said.